Tissue culture might be a method supplementing traditional plant propagation in various fields, like agriculture, medicine, industry, and the active conservation of plant species. For the purpose of plant restoration, it is important that the obtained progenies are identical with the mother plants to ensure the true-to-typeness of the future population. Methods: In the present study, the stability of Aldrovanda vesiculosa regenerants obtained in vitro through phenotypic and genetic analysis was estimated. Clones of aldrovanda plants were cultivated in tissue culture in the 1/10 MS liquid medium under the same conditions for over a year, with five weeks of subculturing. Results: It was observed that two clones formed plants that displayed atypical growth structures, the shoots were shorter with many lateral shoots, and they had a lower fresh weight. They also formed fewer and smaller snap-traps, which, in the case of carnivorous plants, determines the capability of catching prey. The 35 in vitro regenerated plants and 5 specimens obtained from the natural habitat were subjected to genetic analyses with two molecular markers: start codon targeted (SCoT) polymorphism and sequence-related amplified polymorphism (SRAP). Despite the visible morphological variants, the genetic stability of all the regenerants with the individuals from natural stands was confirmed. All of them were monomorphic except three bands that were obtained for reference, where individuals were amplified with SCoT28 and me12-em13 SRAP primers. Conclusions: As shown in the presented research, it might be recommended to use different methods to evaluate the stability of in vitro cultivated plants.